Glyphosate, the key ingredient in Monsanto’s Roundup pesticide, is being linked to damaged soil and roots of treated plants, finds 15 years of study, according to a representative from the USDA.

Fungal root disease has increased among farmers using the popular Roundup pesticide, particularly on the Monsanto genetically modified Roundup Ready seeds, according to Bob Kremer, a microbiologist with the U.S. Department of Agriculture’s Agricultural Research Service.

GM corn and soybeans represent a majority of Roundup dependent crops grown in the U.S., and this “invisible” plight of changes in soil bacteria and increased presence of fungus could indicate larger problems ahead with Monsanto’s Roundup Ready and other GMO seeds. With so many farmers in the U.S. now dependent on glyphosate pesticides and genetically modified seeds, the implications of widespread soil fungus are tremendous as a resistant fungus could devastate farms. The presence of newly discovered glyphosate resistant “superweeds” are already taking a toll on farmers’ crops and machinery.

The research also revealed that the controversial genetically altered crops are not showing signs of yielding more than conventional crops, despite that being one of the key selling points of genetically modified seed manufacturers including Monsanto. Nutrient deficiencies linked to the root disease problems are likely a limiting factor, Kremer says, and the fungal diseases could limit crop health and production even further in the future warranting significantly more research.

Among the growing concerns over heavy use of glyphosate based pesticides are links to human and livestock health risks including cancer, fertility issues, birth defects, organ damage and neurological disorders.